1302990
doi
10.5281/zenodo.1302990
oai:zenodo.org:1302990
slimsuite/SLiMSuite: SLiMSuite v1.4.0 (2018-07-02)
Richard J Edwards
UNSW
url:https://github.com/slimsuite/SLiMSuite/tree/v1.4.0
info:eu-repo/semantics/openAccess
Other (Open)
<p>This release of SLiMSuite contains a number of updates related to the <a href="http://rest.slimsuite.unsw.edu.au/">REST servers</a> and some new pre-release dev tools in the main repo (but not the <code>*.tgz</code> file).</p>
<p><strong>SeqList</strong> has updated sequence summary statistics and grep-based redundancy removal for large genomes.</p>
<p>One major bug fix is a change to parsing Uniprot entries from the website following a change in behaviour of the API.</p>
<p>SLiMSuite updates</p>
<p>Updates in extras/:</p>
<p> </p>
<p><strong>• rje_pydocs:</strong> <em>Updated from Version 2.16.3.</em><br>
→ Version 2.16.4: Tweaked formatDocString.<br>
→ Version 2.16.5: Added general commands to docstring HTML for REST servers.<br>
→ Version 2.16.6: Modified parsing to keep DocString for SPyDarm runs.<br>
→ Version 2.16.7: Fixed T/F/FILE option type parsing bug.</p>
<p> </p>
<p>Updates in libraries/:</p>
<p> </p>
<p><strong>• rje_blast_V2:</strong> <em>Updated from Version 2.18.0.</em><br>
→ Version 2.19.0: Added blastgz=T/F : Whether to zip and unzip BLAST results files [False]<br>
→ Version 2.19.1: Fixed erroneous i=-1 blastprog over-ride but not sure why it was happening.<br>
→ Version 2.20.0: Added localGFF output<br>
→ Version 2.21.0: Added blasttask=X setting for BLAST -task ['megablast']<br>
→ Version 2.22.0: Added dust filter for blastn and setting blastprog based on blasttask<br>
→ Version 2.22.1: Added trimLocal error catching for exonerate issues.<br>
→ Version 2.22.2: Fixed GFF attribute case issue.</p>
<p><strong>• rje_db:</strong> <em>Updated from Version 1.8.6.</em><br>
→ Version 1.9.0: Added comment output to saveToFile().</p>
<p><strong>• rje_disorder:</strong> <em>Updated from Version 0.8.</em><br>
→ Version 1.0.0: Added random disorder function and elevated to v1.x as fully functional for SLiMSuite<br>
→ Version 1.1.0: Added strict option for disorder method selection. Added minorder=X.<br>
→ Version 1.2.0: Added saving and loading scores to IUScoreDir/.</p>
<p><strong>• rje_gff:</strong> <em>Created/Renamed/moved.</em><br>
→ Version 0.0.0: Initial Compilation.<br>
→ Version 0.1.0: Basic functional version.</p>
<p><strong>• rje_hpc:</strong> <em>Updated from Version 1.1.</em><br>
→ Version 1.1.1: Added output of subjob command to log as run.</p>
<p><strong>• rje_html:</strong> <em>Updated from Version 0.2.1.</em><br>
→ Version 0.3.0: Added optional loading of javascript files and stupidtable.js?dev default.</p>
<p><strong>• rje_qsub:</strong> <em>Updated from Version 1.9.1.</em><br>
→ Version 1.9.2: Modified qsub() to return job ID.</p>
<p><strong>• rje_samtools:</strong> <em>Updated from Version 1.19.2.</em><br>
→ Version 1.20.0: Added parsing of BAM file - needs samtools on system. Added minsoftclip=X, maxsoftclip=X and minreadlen=X.</p>
<p><strong>• rje_seq:</strong> <em>Updated from Version 3.24.0.</em><br>
→ Version 3.25.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]</p>
<p><strong>• rje_seqlist:</strong> <em>Updated from Version 1.25.0.</em><br>
→ Version 1.26.0: Updated sequence statistics and fixed N50 underestimation bug.<br>
→ Version 1.26.1: Fixed median length overestimation bug.<br>
→ Version 1.26.2: Fixed sizesort bug. (Now big to small as advertised.)<br>
→ Version 1.27.0: Added grepNR() method (dev only). Switched default to RevCompNR=T.<br>
→ Version 1.28.0: Fixed second pass NR naming bug and added option to switch off altogether.<br>
→ Version 1.29.0: Added maker=T/F : Whether to extract MAKER2 statistics (AED, eAED, QI) from sequence names [False]</p>
<p><strong>• rje_slimcalc:</strong> <em>Updated from Version 0.9.3.</em><br>
→ Version 0.10.0: Added extra disorder methods to slimcalc.</p>
<p><strong>• rje_taxonomy:</strong> <em>Updated from Version 1.2.0.</em><br>
→ Version 1.3.0: taxtable=T/F : Whether to output results in a table rather than text lists [False]</p>
<p><strong>• rje_tree:</strong> <em>Updated from Version 2.15.0.</em><br>
→ Version 2.16.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]<br>
→ Version 2.16.1: Modified NSF reading to cope with extra information beyond the ";".</p>
<p><strong>• rje_uniprot:</strong> <em>Updated from Version 3.24.1.</em><br>
→ Version 3.24.2: Updated HTTP to HTTPS. Having some download issues with server failures.<br>
→ Version 3.25.0: Fixed new Uniprot batch query URL. Added onebyone=T/F : Whether to download one entry at a time. Slower but should maintain order [False].</p>
<p><strong>• rje_zen:</strong> <em>Updated from Version 1.3.2.</em><br>
→ Version 1.4.0: Added some more words and "They fight crime!" structure.</p>
<p>Updates in tools/:</p>
<p> </p>
<p><strong>• gablam:</strong> <em>Updated from Version 2.28.3.</em><br>
→ Version 2.29.0: Added localGFF=T/F output</p>
<p><strong>• gasp:</strong> <em>Updated from Version 1.4.</em><br>
→ Version 2.0.0: Upgraded to rje_obj framework for REST server.</p>
<p><strong>• gasp_V1:</strong> <em>Created/Renamed/moved.</em><br>
→ Version 0.0: Initial Compilation.<br>
→ Version 1.0: Improved version with second pass.<br>
→ Version 1.1: Improved OO. Restriction to descendant AAs. (Good for BAD etc.)<br>
→ Version 1.2: No Out Object in Objects<br>
→ Version 1.3: Added more interactive load options<br>
→ Version 1.4: Minor tweaks to imports.</p>
<p><strong>• gopher:</strong> <em>Updated from Version 3.4.2.</em><br>
→ Version 3.4.3: Added checking and warning if no bootstraps for orthtree.</p>
<p><strong>• haqesac:</strong> <em>Updated from Version 1.11.0.</em><br>
→ Version 1.12.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]</p>
<p><strong>• multihaq:</strong> <em>Updated from Version 1.3.0.</em><br>
→ Version 1.4.0: Added SLiMFarmer batch forking if autoskip=F and i=-1.<br>
→ Version 1.4.1: Added haqblastdir=PATH: Directory in which MultiHAQ BLAST2FAS BLAST runs will be performed [./HAQBLAST/]</p>
<p><strong>• pagsat:</strong> <em>Updated from Version 2.3.3.</em><br>
→ Version 2.3.4: Fixed full.fas request bug.<br>
→ Version 2.4.0: Added PAGSAT compile mode to generate comparisons of reference chromosomes across assemblies.</p>
<p><strong>• seqsuite:</strong> <em>Updated from Version 1.14.0.</em><br>
→ Version 1.14.1: Added zentest for testing the REST servers.<br>
→ Version 1.15.0: Added GASP to REST servers.<br>
→ Version 1.16.0: Add rje_gff.GFF to REST servers.<br>
→ Version 1.17.0: Added batch summarise mode.<br>
→ Version 1.18.0: Added rje_apollo.Apollo to REST servers.<br>
→ Version 1.19.0: Tweaked the output of batch summarise, adding Gap% and reducing dp for some fields.<br>
→ Version 1.19.1: Fixed GapPC summarise output to be a percentage, not a fraction.</p>
<p><strong>• slimbench:</strong> <em>Updated from Version 2.14.0.</em><br>
→ Version 2.14.1: Fixed up PPIBench results loading.<br>
→ Version 2.14.2: Fixed ByCloud bug.<br>
→ Version 2.15.0: Updated assessSearchMemSaver() to handle different data types properly. dombench not yet supported.<br>
→ Version 2.16.0: Added ppi hub/slim summary and motif filter for assessment datasets post-rating (still count as OT)<br>
→ Version 2.16.1: Bug-fixing PPI generation from pairwise PPI files.<br>
→ Version 2.16.2: Fixed benchmarking setup bug.<br>
→ Version 2.16.3: Fixed bug when Hub-PPI links fail during PPI Benchmarking.<br>
→ Version 2.17.0: Added output of missing datasets when balanced=T.<br>
→ Version 2.18.0: Added dev OccBench with improved ratings and more efficient results handling. (dev only)<br>
→ Version 2.18.1: Added additional OccBench options (bymotif, occsource, occspec)<br>
→ Version 2.18.2: Fixed problem with source file selection ignoring i=-1.</p>
<p><strong>• slimfarmer:</strong> <em>Updated from Version 1.7.0.</em><br>
→ Version 1.8.0: jobforks=X : Number of forks to pass to farmed out run if >0 [0]<br>
→ Version 1.9.0: daisychain=X : Chain together a set of qsub runs of the same call that depend on the previous job.</p>
<p><strong>• slimfinder:</strong> <em>Updated from Version 5.3.3.</em><br>
→ Version 5.3.4: Fixed terminal (^/$) musthave bug.</p>
<p><strong>• slimsuite:</strong> <em>Updated from Version 1.7.0.</em><br>
→ Version 1.7.1: Added error raising for protected REST alias data.</p>
<p><strong>• smrtscape:</strong> <em>Updated from Version 2.2.1.</em><br>
→ Version 2.2.2: Added dna=T to all SeqList object generation.</p>
<p><strong>• snapper:</strong> <em>Updated from Version 1.6.0.</em><br>
→ Version 1.6.1: Fixed bug for reducing to unique-unique pairings that was over-filtering.</p>
<p>© RJ Edwards 2018. Last modified 2 Jul 2018.</p>
<p> </p>
Zenodo
2018-07-02
info:eu-repo/semantics/other
593828
v1.4.0
1641955232.667352
17690377
md5:6d90d2e01f3fd0855c080c4423e9bd56
https://zenodo.org/records/1302990/files/slimsuite/SLiMSuite-v1.4.0.zip
public
https://github.com/slimsuite/SLiMSuite/tree/v1.4.0
Is supplement to
url
10.5281/zenodo.593828
isVersionOf
doi